In the conclusion of Franny and Zooey, Franny effectively resolves her crisis. As Zooey finishes speaking, we read that "for joy, apparently, it was all Franny could do to hold the phone, even with both hands" (Zooey.8.78). After he hangs up, Franny sits and listens to the dial tone as though it is "extraordinarily beautiful" (Zooey.8.80). (Check out "Symbols, Imagery, Allegory" for a discussion on beauty – it seems that Franny has here learned, as her brother did, to appreciate beauty in the world.) Finally, we read that she will eventually fall into "deep, dreamless sleep" (last paragraph). We're left to conclude that Franny is all better.
But why? What happened? How exactly did she resolve her crisis? All of what Zooey said to Franny – first in the living room and then over the phone – played a part in helping her through this rough patch. His lesson to her is many-sided and complex. We talk about it more in Zooey's "Character Analysis," but in brief, he shows her the hypocrisy inherent in her view of the world and reveals the spirituality and joy that can be found in normal events and in every kind of person. (The "Fat Lady" has a lot to do with it, too – see "Symbols, Imagery, Allegory" for more on this.) The point is that Franny reaches resolution, or enlightenment, or peace – whichever of these interpretations you prefer – through Zooey's guidance.
What's interesting is that Franny doesn't take her brother's advice to heart when they are in the living room together. Instead, she yells at him to shut up and buries her face sobbing into the couch. So why does he get through to her over the phone?
Franny's barriers seem to break down when she thinks she is talking to Buddy. She actually responds to Zooey's living room comments, it's just that she thinks she's giving this response to someone else. Remember Zooey's claim that the Glass siblings never converse; rather, they lecture or "hold forth." And he's right; the only way Franny can really have a dialogue with Zooey is by narrating his argument – and then adding her own retort – to a third party.
Perhaps more significant is the influence of both Buddy and Seymour in this phone conversation. In the living room, Franny told Zooey that she wanted to talk to Seymour on the phone. And in a way, she does. By passing on Seymour's story of the "Fat Lady," Zooey channels his older brother's wisdom to his little sister. And of course, by pretending to be Buddy, he channels him as well. All three of these boys play a role in getting Franny back on track.
Lastly, remember that "Franny" and "Zooey" were written independently as two short stories. As such, "Franny" has its own 'ending' (though it's now the middle of the composite novel) to discuss. It's interesting to compare the ending of "Franny" with that of "Zooey." They both conclude with Franny lying down and looking up at the ceiling. (Zooey does a fair bit of ceiling-staring himself, which is something interesting to consider.) But compare the final lines from each. In "Franny": "Her lips began to move, forming soundless words, and they continued to move." In "Zooey": "For some minutes, before she fell into a deep, dreamless sleep, she just lay quiet, smiling at the ceiling."
In the first ending, we gather that Franny is mouthing the words to the Jesus Prayer. In the second, however, she is lying "quiet," which could mean a few different things. Zooey had explained to his mother that, if a person says the prayer enough, he achieves a sort of enlightenment; "The idea, really," he says, "is that sooner or later, completely on its own, the prayer moves from the lips and the head down to a center in the heart and becomes an automatic function in the person, right along with the heartbeat" (Zooey.5.78). This could be what has happened to Franny at the end of the story. She doesn't need to mouth the prayer any more because it's become part of her being.
Another possibility is that Franny has abandoned the Jesus Prayer. Zooey taught her, by using Seymour's story of the "Fat Lady" and his own ideas on Bessie's consecrated chicken soup (again, see "Symbols, Imagery, Allegory") that Christ is everywhere and that holiness can be found in ordinary objects. Franny may have decided that she doesn't need the Jesus Prayer anymore to feel closer to God or to live a spiritual life.